SpatialDE

Functions

fit(adata[, genes, layer, normalized, ...])	Fits Gaussian processes to genes.
fit_detailed(adata[, genes, layer, ...])	Fits Gaussian processes to genes.
fit_fast(adata[, genes, layer, normalized, ...])	Fits Gaussian processes to genes.
fit_spatial_interactions(adata[, layer, ...])	Estimate magnitude of spatial cell-cell interactions using an SVCA model (ARnol, 2019).
read_spaceranger(spaceranger_out_dir[, ...])	Read 10x SpaceRanger output.
spatial_patterns(adata[, genes, normalized, ...])	Detect spatial patterns of gene expression and assign genes to patterns.
test(adata[, layer, omnibus, spatial_key, ...])	Test for spatially variable genes.
test_spatial_interactions(adata[, layer, ...])	Fit an SVCA model (Arnol, 2019) and test for spatial cell-cell interactions.
tissue_segmentation(adata[, layer, genes, ...])	Segment a spatial transcriptomics dataset into distinct spatial regions.

Classes

GP(value)	An enumeration.
GPControl([gp, ipm, ncomponents, ard, ninducers])	Parameters for Gaussian process fitting.
SGPIPM(value)	An enumeration.
SpatialPatternParameters([nclasses, ...])	Parameters for automated expession histology.
SpatialPatterns(converged, status, labels, ...)	Results of automated expression histology.
TissueSegmentation(converged, status, ...)	Results of tissue segmentation.
TissueSegmentationParameters([nclasses, ...])	Parameters for tissue segmentation.
TissueSegmentationStatus(value)	An enumeration.